chr12-14503872-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024829.6(PLBD1):c.1562G>A(p.Arg521His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024829.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLBD1 | NM_024829.6 | c.1562G>A | p.Arg521His | missense_variant | 11/11 | ENST00000240617.10 | NP_079105.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.1562G>A | p.Arg521His | missense_variant | 11/11 | 1 | NM_024829.6 | ENSP00000240617 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251388Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135858
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.0000605 AC XY: 44AN XY: 727164
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74200
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at